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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[TheiaProk] expose sistr optional inputs to TheiaProk wfs #376

Closed kapsakcj closed 1 month ago

kapsakcj commented 8 months ago

:cool:

:pushpin: Explain the Request

This is low priority, but I just realized that the user does not have the ability to change SISTR optional inputs for the various TheiaProk workflows since the task is within the merlin_magic subworkflow.

:books: Context

Low priority. Not requested by any users AFAIK

:chart_with_upwards_trend: Desired Behavior

Allow user to change optional inputs for SISTR, namely cpu, memory, docker, and the Boolean use_full_cgmlst_db optional input: https://github.com/theiagen/public_health_bioinformatics/blob/c3f3b705bf20349dbec54567442b7ed28fe2a93a/tasks/species_typing/task_sistr.wdl#L16

:information_source: Additional Information

sage-wright commented 4 months ago

And srst2, and other hidden optional inputs inside merlin